#pragma once
#include "ShortReadUtil.h"

/*
 * This class is to simulate the spliced reads given a substring
 */
class SimSplicedRead
{
public:
    SimSplicedRead(const char* oFileN);
    ~SimSplicedRead(void);
    ofstream ofile;
    int noSimRead;
    int readLength;
    int anchorLength;
    int middleLength;
    bool bFastaFormat;
    bool setSimPtr(int readLength, int anchorLength, bool bFastaFormat);
    int simulateReads(const char* ref, const char* refN, int start, int simNo);
    int simulateASplicedRead(const char* ref, const char* refN,\
                             int leftL, int sep, int start, bool revComp);
};
